Mercurial > repos > immuneml > immuneml_tools

comparison README.md @ 3:ed3932e6d616 draft

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"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 16:51:28 +0000
parents 629e7e403e19
children 48569213d91c
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2:9bf78cb6b91d 3:ed3932e6d616
3 https://immuneml.uio.no/ 3 https://immuneml.uio.no/
4 4
5 ## Installation: 5 ## Installation:
6 The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way. 6 The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way.
7 7
8 ### New datatype `iml_dataset` 8 ### New datatype `immuneml_receptors`
9 No matter how you install the tools, you will need to define a new datatype, which is done as follows: 9 No matter how you install the tools, you will need to define a new datatype, which is done as follows:
10 10
11 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set 11 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set
12 ``` 12 ```
13 datatypes_config_file: datatypes_conf.xml 13 datatypes_config_file: datatypes_conf.xml
14 ``` 14 ```
15 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined. 15 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
16 3. Add the following line to your `datatypes_config_file`: 16 3. Add the following line to your `datatypes_config_file`:
17 ``` 17 ```
18 <datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/> 18 <datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>
19 ``` 19 ```
20 The line has to be inside `<registration>` along with the other datatypes. 20 The line has to be inside `<registration>` along with the other datatypes.
21 21
22 ### The immuneML conda package 22 ### The immuneML conda package
23 Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes. 23 Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes.